I may get flack for this, but the X100 is the only camera/lens that I generally use a clear protection filter with, because it allows me to always have the camera ready by not using a cap, and it seals the lens from dust coming through the front, and dust in the lens is a common complaint with this camera.

The cool thing is, if you're willing to spend a little money, the Pentax MH-RC slim hood for their 40mm f2.8 pancake lens fits the X100 perfectly (using a filter adapter from Fuji or ebay,) and you can screw a small, high quality B+W filter into the UNDERSIDE of the hood, so it remains very compact, and only slightly impedes the viewfinder. Plus, the whole thing looks very good and OEM...outside of the Pentax labeling.

If I'm ever concerned about an IQ issue with the filter, I just unscrew the whole thing and throw it in my pocket. Of course, one can also use the Pentax hood without a filter at all, too.

Below is a pic of the hood+filter combo, so you can see what it looks like. The pic is from user Moonshine4Ever on flickr:

Here is a side shot from flickr user 246-You. Note that he used a clear filter with a silver ring on the inside of the hood, which I'm not sure I'd recommend, because reflections may be an issue. Not sure: